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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcgccctgccttctcgggctcgctttgatcattgtgcagtttatctgccctaatttgcggttcgtctcggcggtggatcgattcgcgctagttgtgagtgattaatctgttgtttttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCATGAGCCCAAGACGCTGATGGATAAGGTCGCATACTGGACCGTCAAGTCGC

Basic information

species Zea mays
transcript GRMZM2G125669_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G125669_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g51150.1 (Oryza sativa), 3'ss of exon 1
-------------------------gtacgcgccctgcct----tctcgggctcgctttgatc-attgtgcagtttatctgccc-taatttgcggt--tcgtctcggcggtggatcgattcgcgctagttgtgagtgattaatctgttgtttttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCATGAGCCCAAGACGCTGATGGATAAGGTCGCATACTGGACCGTCAAGTCGC
                          |  |   ||||  |    |||     || | | |||  || |     |  || |  || || |  | | |  | | |||||   |  |    | |||||  |  ||| || |||    | |  ||||    | ||||||||||||| ||||| |||||||| || || || || || |  ||||| | ||||||||||||| | || ||| |||| |||||||||||||||||||
gtacttgcgcttcgctttgctcctgatcggtttcctgtttcgattctgtttgtcccgtagattgatcgccagatcgatgtatccatactccgagatagtaggctcggtccttaacttgt-cgcgcc-gccgtgtgtaattttggtttgattttctccgcagCCATGGGAGACCTACACCGCGGACACTTCGATCGATCTGACGAAGCACCACGTGCCCAAGACGCTGCTCGACAAGATCGCCTACTGGACCGTCAAGTCGC
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|148933362|gb|EC877026.2|EC877026
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
EST: gi|211472274|gb|FL205292.1|FL205292
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGAC-TCACCAGACACCAT
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
EST: gi|148947765|gb|EC893251.2|EC893251
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
EST: gi|211472275|gb|FL205293.1|FL205293
EST:     GTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
genomic: GTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
EST: gi|211472278|gb|FL205296.1|FL205296
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGA
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGA
EST: gi|78114087|gb|DV532476.1|DV532476
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
EST: gi|211472271|gb|FL205289.1|FL205289
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
EST: gi|148960977|gb|EE011674.2|EE011674
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
EST: gi|149015792|gb|EE045489.2|EE045489
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
EST: gi|89250644|gb|DY622430.1|DY622430
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
EST: gi|71439210|gb|DR820260.1|DR820260
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
EST: gi|211472277|gb|FL205295.1|FL205295
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCYTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
EST: gi|148930596|gb|EE285266.2|EE285266
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
EST: gi|211472270|gb|FL205288.1|FL205288
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACAC
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACAC
EST: gi|211472276|gb|FL205294.1|FL205294
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGT
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGT
EST: gi|211472268|gb|FL205286.1|FL205286
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACA
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACA
EST: gi|13150527|gb|BG320849.1|BG320849
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGACYTCACCAGACACCAT
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
EST: gi|211472273|gb|FL205291.1|FL205291
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGT
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGT
EST: gi|211472269|gb|FL205287.1|FL205287
EST:     CAAGCTAGCGCKGTGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCG
genomic: CAAGCTAGCGCGG-GACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCG
EST: gi|148949605|gb|EC895076.2|EC895076
EST:     ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGG                         CCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT
genomic: ACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 152

AGACAAGAAGGCGGTGGTGATCAACAGCTACTGGGGGATCGAGCAAAACAACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCATGAGCCCAAGACGCTGATGGATAAGGTCGCATACTGGACCGTCAAGTCGC


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 41

AGACAAGAAGGCGGTGGTGATCAACAGCTACTGGGGGATCGAGCAAAACAACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCATGAGCCCAAGACGCTGATGGATAAGGTCGCATACTGGACCGTCAAGTCGC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 147

AGACAAGAAGGCGGTGGTGATCAACAGCTACTGGGGGATCGAGCAAAACAACAAGCTAGCGCGGGACGACGGCACCGAGTGGAAGTGGACTTGCTTTAGGgtacgcgccc ... tttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCATGAGCCCAAGACGCTGATGGATAAGGTCGCATACTGGACCGTCAAGTCGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcggtggatcgattcgcgctagttgtgagtgattaatctgttgtttttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCATGAGCCCAAGACGCTGATGGATAAGGTCGCATACTGGACCGTCAAGTCGC
                              gattaat  putative branch site (score: 147)
                                        ttgttttt  putative PPT
                             tgattaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcgccctgccttctcgggctcgctttgatcattgtgcagtttatctgccctaatttgcggttcgtctcggcggtggatcgattcgcgctagttgtgagtgattaatctgttgtttttgttgaagCCATGGGAGACGTACACGGCGGACACGTCCATTGACCTCACCAGACACCATGAGCCCAAGACGCTGATGGATAAGGTCGCATACTGGACCGTCAAGTCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA